The table below highlights all of the cell lines that are included in the analyses and the types that they are annotated as:
devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.2 (2019-12-12)
## os macOS Catalina 10.15.6
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-08-18
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor
## ape 5.3 2019-03-17 [1] CRAN (R 3.6.0)
## askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
## backports 1.1.6 2020-04-05 [1] CRAN (R 3.6.2)
## bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0)
## Biobase 2.46.0 2019-10-29 [1] Bioconductor
## BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor
## BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0)
## BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
## bit 1.1-15.2 2020-02-10 [1] CRAN (R 3.6.0)
## bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
## bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
## blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.0)
## broom 0.5.5 2020-02-29 [1] CRAN (R 3.6.0)
## callr 3.4.3 2020-03-28 [1] CRAN (R 3.6.2)
## caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.6.0)
## cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0)
## cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.2)
## clusterProfiler * 3.14.3 2020-01-08 [1] Bioconductor
## codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.2)
## colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
## cowplot 1.0.0 2019-07-11 [1] CRAN (R 3.6.0)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
## crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 3.6.0)
## data.table * 1.12.8 2019-12-09 [1] CRAN (R 3.6.0)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.0)
## dbplyr 1.4.2 2019-06-17 [1] CRAN (R 3.6.0)
## desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
## devtools 2.3.0 2020-04-10 [1] CRAN (R 3.6.2)
## digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0)
## DO.db 2.9 2020-02-13 [1] Bioconductor
## DOSE 3.12.0 2019-10-29 [1] Bioconductor
## dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0)
## DT * 0.13 2020-03-23 [1] CRAN (R 3.6.0)
## ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
## enrichplot 1.6.1 2019-12-16 [1] Bioconductor
## europepmc 0.3 2018-04-20 [1] CRAN (R 3.6.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.0)
## extrafont * 0.17 2014-12-08 [1] CRAN (R 3.6.0)
## extrafontdb 1.0 2012-06-11 [1] CRAN (R 3.6.0)
## fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)
## farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.0)
## fastmatch 1.1-0 2017-01-28 [1] CRAN (R 3.6.0)
## fgsea 1.12.0 2019-10-29 [1] Bioconductor
## fitdistrplus 1.0-14 2019-01-23 [1] CRAN (R 3.6.0)
## forcats * 0.5.0 2020-03-01 [1] CRAN (R 3.6.0)
## fs 1.4.1 2020-04-04 [1] CRAN (R 3.6.2)
## future 1.16.0 2020-01-16 [1] CRAN (R 3.6.0)
## future.apply 1.4.0 2020-01-07 [1] CRAN (R 3.6.0)
## gbRd 0.4-11 2012-10-01 [1] CRAN (R 3.6.0)
## gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0)
## generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.0)
## ggforce 0.3.1 2019-08-20 [1] CRAN (R 3.6.0)
## ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 3.6.0)
## ggplotify 0.0.5 2020-03-12 [1] CRAN (R 3.6.0)
## ggpubr * 0.2.5 2020-02-13 [1] CRAN (R 3.6.0)
## ggraph 2.0.2 2020-03-17 [1] CRAN (R 3.6.0)
## ggrepel * 0.8.2 2020-03-08 [1] CRAN (R 3.6.0)
## ggridges 0.5.2 2020-01-12 [1] CRAN (R 3.6.0)
## ggsignif 0.6.0 2019-08-08 [1] CRAN (R 3.6.0)
## ggthemes * 4.2.0 2019-05-13 [1] CRAN (R 3.6.0)
## globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0)
## glue 1.4.0 2020-04-03 [1] CRAN (R 3.6.2)
## GO.db 3.10.0 2020-02-13 [1] Bioconductor
## GOSemSim 2.12.1 2020-03-19 [1] Bioconductor
## gplots 3.0.3 2020-02-25 [1] CRAN (R 3.6.0)
## graphlayouts 0.6.0 2020-03-09 [1] CRAN (R 3.6.0)
## gridExtra * 2.3 2017-09-09 [1] CRAN (R 3.6.0)
## gridGraphics 0.5-0 2020-02-25 [1] CRAN (R 3.6.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
## gtools 3.8.2 2020-03-31 [1] CRAN (R 3.6.2)
## haven 2.2.0 2019-11-08 [1] CRAN (R 3.6.0)
## hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.0)
## htmltools * 0.4.0 2019-10-04 [1] CRAN (R 3.6.0)
## htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.0)
## httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0)
## ica 1.0-2 2018-05-24 [1] CRAN (R 3.6.0)
## igraph 1.2.5 2020-03-19 [1] CRAN (R 3.6.0)
## IRanges 2.20.2 2020-01-13 [1] Bioconductor
## irlba 2.3.3 2019-02-05 [1] CRAN (R 3.6.0)
## jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.0)
## KernSmooth 2.23-16 2019-10-15 [1] CRAN (R 3.6.2)
## knitr 1.28 2020-02-06 [1] CRAN (R 3.6.0)
## labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
## lattice 0.20-41 2020-04-02 [1] CRAN (R 3.6.2)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
## leiden 0.3.3 2020-02-04 [1] CRAN (R 3.6.0)
## lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.0)
## limma * 3.42.2 2020-02-03 [1] Bioconductor
## listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0)
## lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0)
## lsei 1.2-0 2017-10-23 [1] CRAN (R 3.6.0)
## lubridate 1.7.8 2020-04-06 [1] CRAN (R 3.6.2)
## magrittr * 1.5 2014-11-22 [1] CRAN (R 3.6.0)
## MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.0)
## Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2)
## matrixStats * 0.56.0 2020-03-13 [1] CRAN (R 3.6.0)
## memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
## metap 1.3 2020-01-23 [1] CRAN (R 3.6.0)
## mgcv 1.8-31 2019-11-09 [1] CRAN (R 3.6.2)
## mnormt 1.5-6 2020-02-03 [1] CRAN (R 3.6.0)
## modelr 0.1.6 2020-02-22 [1] CRAN (R 3.6.0)
## multcomp 1.4-13 2020-04-08 [1] CRAN (R 3.6.2)
## multtest 2.42.0 2019-10-29 [1] Bioconductor
## munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
## mutoss 0.1-12 2017-12-04 [1] CRAN (R 3.6.0)
## mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 3.6.0)
## nlme 3.1-145 2020-03-04 [1] CRAN (R 3.6.0)
## npsurv 0.4-0 2017-10-14 [1] CRAN (R 3.6.0)
## numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)
## openssl 1.4.1 2019-07-18 [1] CRAN (R 3.6.0)
## patchwork 1.0.0 2019-12-01 [1] CRAN (R 3.6.0)
## pbapply * 1.4-2 2019-08-31 [1] CRAN (R 3.6.0)
## pheatmap * 1.0.12 2019-01-04 [1] CRAN (R 3.6.0)
## pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0)
## pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0)
## pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
## plotly * 4.9.2.1 2020-04-04 [1] CRAN (R 3.6.2)
## plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0)
## plyr * 1.8.6 2020-03-03 [1] CRAN (R 3.6.0)
## png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0)
## polyclip 1.10-0 2019-03-14 [1] CRAN (R 3.6.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2)
## processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0)
## progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0)
## ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0)
## purrr * 0.3.3 2019-10-18 [1] CRAN (R 3.6.0)
## qvalue 2.18.0 2019-10-29 [1] Bioconductor
## R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0)
## RANN 2.6.1 2019-01-08 [1] CRAN (R 3.6.0)
## RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
## Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.2)
## RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 3.6.0)
## Rdpack 0.11-1 2019-12-14 [1] CRAN (R 3.6.0)
## readr * 1.3.1 2018-12-21 [1] CRAN (R 3.6.0)
## readxl * 1.3.1 2019-03-13 [1] CRAN (R 3.6.0)
## remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.0)
## reprex 0.3.0 2019-05-16 [1] CRAN (R 3.6.0)
## reshape2 1.4.4 2020-04-09 [1] CRAN (R 3.6.2)
## reticulate 1.15 2020-04-02 [1] CRAN (R 3.6.2)
## rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0)
## rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.6.0)
## ROCR 1.0-7 2015-03-26 [1] CRAN (R 3.6.0)
## rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
## RSpectra 0.16-0 2019-12-01 [1] CRAN (R 3.6.0)
## RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.0)
## rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0)
## rsvd 1.0.3 2020-02-17 [1] CRAN (R 3.6.0)
## Rtsne * 0.15 2018-11-10 [1] CRAN (R 3.6.0)
## Rttf2pt1 1.3.8 2020-01-10 [1] CRAN (R 3.6.0)
## rvcheck 0.1.8 2020-03-01 [1] CRAN (R 3.6.0)
## rvest 0.3.5 2019-11-08 [1] CRAN (R 3.6.0)
## S4Vectors 0.24.4 2020-04-09 [1] Bioconductor
## sandwich 2.5-1 2019-04-06 [1] CRAN (R 3.6.0)
## scales * 1.1.0 2019-11-18 [1] CRAN (R 3.6.0)
## sctransform 0.2.1 2019-12-17 [1] CRAN (R 3.6.0)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
## Seurat * 3.1.4 2020-02-26 [1] CRAN (R 3.6.0)
## sn 1.6-1 2020-04-01 [1] CRAN (R 3.6.2)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0)
## stringr * 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
## survival 3.1-12 2020-04-10 [1] CRAN (R 3.6.2)
## testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.0)
## TFisher 0.2.0 2018-03-21 [1] CRAN (R 3.6.0)
## TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.0)
## tibble * 3.0.0 2020-03-30 [1] CRAN (R 3.6.2)
## tidygraph 1.1.2 2019-02-18 [1] CRAN (R 3.6.0)
## tidyr * 1.0.2 2020-01-24 [1] CRAN (R 3.6.2)
## tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.2)
## tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 3.6.0)
## triebeard 0.3.0 2016-08-04 [1] CRAN (R 3.6.0)
## tsne 0.1-3 2016-07-15 [1] CRAN (R 3.6.0)
## tweenr 1.0.1 2018-12-14 [1] CRAN (R 3.6.0)
## umap * 0.2.5.0 2020-03-09 [1] CRAN (R 3.6.0)
## urltools 1.7.3 2019-04-14 [1] CRAN (R 3.6.0)
## usethis 1.6.0 2020-04-09 [1] CRAN (R 3.6.2)
## uwot 0.1.8 2020-03-16 [1] CRAN (R 3.6.0)
## vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.0)
## viridis 0.5.1 2018-03-29 [1] CRAN (R 3.6.0)
## viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0)
## withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
## xfun 0.13 2020-04-13 [1] CRAN (R 3.6.2)
## xml2 1.3.1 2020-04-09 [1] CRAN (R 3.6.2)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.0)
## zoo 1.8-7 2020-01-10 [1] CRAN (R 3.6.0)
##
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library